I recently got a 89 mustang gt
Car seems a bit heavy tried dumping engine codes the only method that worked was jumping it to the neg side of the battery
Cleaned the maf and IAC
It also has time starting in the morning turns off then shuts off
Also tranny throws reverse unless u hold it..
Has after market shifter
Smoke and water come out from passenger tail pipe(has exhaust leak from same tail pipe right under shifter

Were you able to retrieve any codes?
Does the smoke and water from the tail pipe continue after the car has been driven for a while?
Is there coolant that is mysteriously disappearing form the radiator?

That is a lot of codes to have all at once!
I'm wondering if the engine has been worked on recently and maybe some of the sensors did not get properly connected?
Or possibly the wiring harness is damaged, or the connection at the PCM is loose or corroded?

I would start by checking the wiring and connectors to each of the sensors on top of the intake manifold. It seems like every one of them is throwing a code. Carefully inspect that entire wiring harness to make sure that it isn't damaged and all of the sensors are properly connected.

Did you have the transmission in neutral & the ac off when you ran the koeo test??If yes,you need to troubleshoot code 67 first.Its related to the NSS circuit(which is used for idle control strategy)& having this code logged in a manual transmission equipped Mustang will cause stalling,idle surge & rolling idle.The EEC uses the NSS circuit for idle control,so it has to be able to id a "in neutral condition" anytime the clutch pedal is depressed & anytime the shifter is placed in neutral,otherwise the engine will stall.If code 67 is logged as a failure,it wont let the koer test begin,due to safety reasons.So in otherwords,you'll have to eliminate the cause for code 67 before you'll be able to run the koer test.The following link will help you troubleshoot code 67.NSS/Clutch Pedal Switch Code 67 Troubleshooting

The fact that you had to use the alternate connection method to run the koeo test is usually a sign that there's an issue with the signal return circuit,either between the vip connecter & the eec 60 pin connecter or inside the eec itself.When you connect the jumper wire to the top right terminal on the VIP connecter or you connect the scanner to the VIP connecter, you're using the signal return line.If the methods above don't trigger the tests to begin,but connecting the jumper wire to the (-) battery post allows the test to begin,that tells you the signal return is open.
Another thing that leads me to believe the signal return line is open relates to the multiple codes you've got.
TPS(code 51)
ECT(code 53)
ACT(code 54)
EVP(code 35)
BP (code 22)
Every single one of these sensors uses/shares the same signal return line.Anytime you've got all of these codes present,on top of,not being able to use a scanner or jumper wire at the VIP connecter tells me 100% that you've got a blown/melted signal return trace on the EEC circuit board.I'll post pictures below & a link so you can see what this condition looks like & how you can repair it yourself with a soldering gun and tiny gauge wire.After you remove your EEC from the passenger kick panel and take the back cover off of it,make sure you inspect the 3 blue capacitors too.One last thing I recommend doing is the salt & pepper shakers maintenance.All of the sensors( you've got codes stored for)listed above has 1 or 2 of their wires passing through the salt & pepper shakers,so you could also have loose or corroded pinouts on these connecters causing your codes.The following link will help.Salt & Pepper (10-pin) Connectors Fix

You might also wanna take a look at your o2 sensor harness.Make sure its a manual o2 harness & not an auto o2 harness.Here's why::

Auto O2 harness = neutral safety switch and presence of 12 volts when you're cranking the engine.
Manual O2 harness = SIGRTN is sourced through the clutch pedal and trans gear switch so no voltage is present.If you use an auto transmission O2 harness on a Mustang that uses the clutch pedal switch,the SIGRTN line will get blasted with 12 volts everytime you press the clutch pedal down.
So make sure you've got the correct harness before you reinstall the repaired or purchased EEC.If you go buy a new EEC & reinstall it & the previous owner has the wrong o2 harness installed, you'll blow the signal return line again on the new EEC.Your car might have the correct harness installed already, but you need to double check because this is the #1 thing that causes the line to blow in the first place.Somebody accidentally installs the wrong harness & then they wonder why all of these codes are present & why a scanner can't be used to run codes.
BTW-the 1st picture below is a AUTO o2 harness & the 2nd picture is a MANUAL o2 harness.Make sure yours looks like picture #2,if your car uses the clutch pedal switch shown in the code 67 trouble shooting link.

It also has time starting in the morning turns off then shuts off
Also tranny throws reverse unless u hold it..
Has after market shifterAttachment 194983

If the 3 blue capacitors are leaking on your EEC board,that can cause the hard starting.
If your aftermarket shifter has stop bolts,the rear stop bolt probably needs to be adjusted outward,away from the shifter handle.The stop bolts screw into the shifter base then you turn them inwards to prevent you from over throwing the shifter handle & you do just the opposite if the shifter is popping out of gear.Just remove that plastic bezel from around the shifter & you should see these stop bolts.